rs1415771

Homo sapiens
G>A
EDEM2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0480 (14342/29824,GnomAD)
A=0498 (14519/29118,TOPMED)
A=0449 (2251/5008,1000G)
A=0455 (1755/3854,ALSPAC)
A=0473 (1755/3708,TWINSUK)
chr20:35146690 (GRCh38.p7) (20q11.22)
AD
GWASdb2
1   publication(s)
See rs on genome
14 Enhancers around
18 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.35146690G>A
GRCh37.p13 chr 20NC_000020.10:g.33734493G>A

Gene: EDEM2, ER degradation enhancing alpha-mannosidase like protein 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
EDEM2 transcript variant 2NM_001145025.1:c.N/AIntron Variant
EDEM2 transcript variant 1NM_018217.2:c.N/AIntron Variant
EDEM2 transcript variant 3NR_026728.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.387A=0.613
1000GenomesAmericanSub694G=0.720A=0.280
1000GenomesEast AsianSub1008G=0.712A=0.288
1000GenomesEuropeSub1006G=0.574A=0.426
1000GenomesGlobalStudy-wide5008G=0.551A=0.449
1000GenomesSouth AsianSub978G=0.460A=0.540
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.545A=0.455
The Genome Aggregation DatabaseAfricanSub8678G=0.411A=0.589
The Genome Aggregation DatabaseAmericanSub836G=0.750A=0.250
The Genome Aggregation DatabaseEast AsianSub1606G=0.717A=0.283
The Genome Aggregation DatabaseEuropeSub18402G=0.542A=0.458
The Genome Aggregation DatabaseGlobalStudy-wide29824G=0.519A=0.480
The Genome Aggregation DatabaseOtherSub302G=0.520A=0.480
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.501A=0.498
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.527A=0.473
PMID Title Author Journal
23089632A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53.Wang JCMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs14157715.03E-06alcohol dependence23089632

eQTL of rs1415771 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr20:33734493MAP1LC3AENSG00000101460.8G>A7.8389e-21599835Cerebellum
Chr20:33734493ACSS2ENSG00000131069.15G>A9.5705e-8274544Cerebellum
Chr20:33734493MYH7BENSG00000078814.11G>A1.6270e-10171287Cerebellum
Chr20:33734493MAP1LC3AENSG00000101460.8G>A1.0998e-10599835Cortex
Chr20:33734493MAP1LC3AENSG00000101460.8G>A1.3972e-11599835Cerebellar_Hemisphere

meQTL of rs1415771 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr203373875133738914E0684258
chr203375394933754653E06919456
chr203371963533720004E070-14489
chr203372013933720189E070-14304
chr203372046833720524E070-13969
chr203372075333721019E070-13474
chr203375394933754653E07019456
chr203377944133779565E07044948
chr203377959933779675E07045106
chr203373246633733582E071-911
chr203375394933754653E07119456
chr203375901133759335E07224518
chr203375394933754653E07419456
chr203375394933754653E08219456







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr203373402733735715E0670
chr203373402733735715E0680
chr203375936033760317E06824867
chr203373402733735715E0690
chr203375936033760317E06924867
chr203373402733735715E0700
chr203375936033760317E07024867
chr203376251733762924E07028024
chr203373402733735715E0710
chr203375936033760317E07124867
chr203376062133760686E07126128
chr203373402733735715E0720
chr203375936033760317E07224867
chr203373402733735715E0730
chr203373402733735715E0740
chr203375936033760317E07424867
chr203373402733735715E0810
chr203373402733735715E0820